| 1. |
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
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| 4. |
- Kristan, Matej, et al.
(författare)
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The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
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Ingår i: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 5. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 6. |
- Stanaway, Jeffrey D., et al.
(författare)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
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Ingår i: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
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Tidskriftsartikel (refereegranskat)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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| 7. |
- Ades, M., et al.
(författare)
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Global Climate : in State of the climate in 2019
- 2020
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Ades, M., et al.
(författare)
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GLOBAL CLIMATE
- 2020
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Ingår i: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
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Tidskriftsartikel (refereegranskat)
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| 9. |
- Argirion, Ilona, et al.
(författare)
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Comparative Analysis of the Humoral Immune Response to the EBV Proteome across EBV-Related Malignancies
- 2023
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association For Cancer Research (AACR). - 1055-9965 .- 1538-7755. ; 32:5, s. 687-696
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Tidskriftsartikel (refereegranskat)abstract
- Background: Epstein-Barr virus (EBV) is linked to multiple cancers, including classical Hodgkin lymphoma (cHL), endemic Burkitt lymphoma (eBL), nasopharyngeal carcinoma (NPC), and extranodal natural killer/T-cell lymphoma (NKTCL).Methods: Anti-EBV IgG and IgA antibody responses target-ing 202 sequences from 86 EBV proteins were measured using the same EBV whole proteome array across four case-control studies investigating EBV-positive cHL, eBL, NPC, and NKTCL (407 cases/620 controls). We grouped EBV-targeted antibodies into pathways by immunoglobulin type (IgA and IgG) and life-cycle stage (latent, immediate early lytic, early lytic, late lytic, and glycoprotein) and evaluated their associ-ation with each cancer type. In an additional analysis, we focused on the subset of 46 individual antibodies repre-senting the top candidates for each cancer and compared their associations across the four cancer types using multivariable linear regression models.Results: IgA antibody responses targeting all EBV life-cycle stages were associated with NPC but limited to anti-early lytic stage for cHL. NPC and eBL were associated with IgG antibodies across the viral life cycle; cHL with antibodies in the early lytic, late lytic and glyco-protein stages; and NKTCL with antibodies in the latent, immediate early lytic and early lytic phases. EBNA3A, BBLF1, BDLF4, and BLRF2 IgG antibodies were associated with all cancer types.Conclusions: Our observed similarities and differences across four EBV-associated cancers may inform EBV-related oncogenesis.Impact: Understanding the comparative humoral immune response across EBV-related cancers may aid in identifying shared etiologic roles of EBV proteins and inform unique pathogenic processes for each cancer.
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| 10. |
- Chan, Ding Cheng Derrick, et al.
(författare)
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Consensus on best practice standards for Fracture Liaison Service in the Asia-Pacific region
- 2018
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Ingår i: Archives of Osteoporosis. - : Springer Science and Business Media LLC. - 1862-3522 .- 1862-3514. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Summary: The Fracture Liaison Service (FLS) Consensus Meeting endorsed by the International Osteoporosis Foundation (IOF), Asian Federation of Osteoporosis Societies (AFOS), and Asia Pacific Osteoporosis Foundation (APOF) was hosted by the Taiwanese Osteoporosis Association on October 14, 2017. International and domestic experts reviewed the 13 Best Practice Framework (BPF) standards and concluded that all standards were generally applicable in the Asia-Pacific region and needed only minor modifications to fit the healthcare settings in the region. Purpose: To review and generate consensus on best practices of fracture liaison service (FLS) in the Asia-Pacific (AP) region. Methods: In October 2017, the Taiwanese Osteoporosis Association (TOA) invited experts from the AP region (n = 23), the Capture the Fracture Steering Committee (n = 2), and the USA (n = 1) to join the AP region FLS Consensus Meeting in Taipei. After two rounds of consensus generation, the recommendations on the 13 Best Practice Framework (BPF) standards were reported and reviewed by the attendees. Experts unable to attend the on-site meeting reviewed the draft, made suggestions, and approved the final version. Results: Because the number of FLSs in the region is rapidly increasing, experts agreed that it was timely to establish consensus on benchmark quality standards for FLSs in the region. They also agreed that the 13 BPF standards and the 3 levels of standards were generally applicable, but that some clarifications were necessary. They suggested, for example, that patient and family education be incorporated into the current standards and that communication with the public to promote FLSs be increased. Conclusions: The consensus on the 13 BPF standards reviewed in this meeting was that they were generally applicable and required only a few advanced clarifications to increase the quality of FLSs in the region.
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| 11. |
- Dunn, R. J. H., et al.
(författare)
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GLOBAL CLIMATE : State of the Climate in 2020
- 2021
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Ingår i: Bulletin of the American Meteorological Society. - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 102:8
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Tidskriftsartikel (refereegranskat)
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| 12. |
- Flood, Padraic, et al.
(författare)
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Natural variation in phosphorylation of photosystem II proteins in Arabidopsis thaliana: is it caused by genetic variation in the STN kinases?
- 2014
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 369:1640
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Tidskriftsartikel (refereegranskat)abstract
- Reversible phosphorylation of photosystem II (PSII) proteins is an important regulatory mechanism that can protect plants from changes in ambient light intensity and quality. We hypothesized that there is natural variation in this process in Arabidopsis (Arabidopsis thaliana), and that this results from genetic variation in the STN7 and STN8 kinase genes. To test this, Arabidopsis accessions of diverse geographical origins were exposed to two light regimes, and the levels of phospho-D1 and phospho-light harvesting complex II (LHCII) proteins were quantified by western blotting with anti-phosphothreonine antibodies. Accessions were classified as having high, moderate or low phosphorylation relative to Col-0. This variation could not be explained by the abundance of the substrates in thylakoid membranes. In genotypes with atrazine-resistant forms of the D1 protein, low D1 and LHCII protein phosphorylation was observed, which may be due to low PSII efficiency, resulting in reduced activation of the STN kinases. In the remaining genotypes, phospho-D1 levels correlated with STN8 protein abundance in high-light conditions. In growth light, D1 and LHCII phosphorylation correlated with longitude and in the case of LHCII phosphorylation also with temperature variability. This suggests a possible role of natural variation in PSII protein phosphorylation in the adaptation of Arabidopsis to diverse environments.
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| 13. |
- Fullman, N., et al.
(författare)
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Measuring performance on the Healthcare Access and Quality Index for 195 countries and territories and selected subnational locations: a systematic analysis from the Global Burden of Disease Study 2016
- 2018
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Ingår i: Lancet. - : Elsevier BV. - 0140-6736. ; 391:10136, s. 2236-2271
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Tidskriftsartikel (refereegranskat)abstract
- Background A key component of achieving universal health coverage is ensuring that all populations have access to quality health care. Examining where gains have occurred or progress has faltered across and within countries is crucial to guiding decisions and strategies for future improvement. We used the Global Burden of Diseases, Injuries, and Risk Factors Study 2016 (GBD 2016) to assess personal health-care access and quality with the Healthcare Access and Quality (HAQ) Index for 195 countries and territories, as well as subnational locations in seven countries, from 1990 to 2016. Methods Drawing from established methods and updated estimates from GBD 2016, we used 32 causes from which death should not occur in the presence of effective care to approximate personal health-care access and quality by location and over time. To better isolate potential effects of personal health-care access and quality from underlying risk factor patterns, we risk-standardised cause-specific deaths due to non-cancers by location-year, replacing the local joint exposure of environmental and behavioural risks with the global level of exposure. Supported by the expansion of cancer registry data in GBD 2016, we used mortality-to-incidence ratios for cancers instead of risk-standardised death rates to provide a stronger signal of the effects of personal health care and access on cancer survival. We transformed each cause to a scale of 0-100, with 0 as the first percentile (worst) observed between 1990 and 2016, and 100 as the 99th percentile (best); we set these thresholds at the country level, and then applied them to subnational locations. We applied a principal components analysis to construct the HAQ Index using all scaled cause values, providing an overall score of 0-100 of personal health-care access and quality by location over time. We then compared HAQ Index levels and trends by quintiles on the Socio-demographic Index (SDI), a summary measure of overall development. As derived from the broader GBD study and other data sources, we examined relationships between national HAQ Index scores and potential correlates of performance, such as total health spending per capita. Findings In 2016, HAQ Index performance spanned from a high of 97.1 (95% UI 95.8-98.1) in Iceland, followed by 96.6 (94.9-97.9) in Norway and 96.1 (94.5-97.3) in the Netherlands, to values as low as 18.6 (13.1-24.4) in the Central African Republic, 19.0 (14.3-23.7) in Somalia, and 23.4 (20.2-26.8) in Guinea-Bissau. The pace of progress achieved between 1990 and 2016 varied, with markedly faster improvements occurring between 2000 and 2016 for many countries in sub-Saharan Africa and southeast Asia, whereas several countries in Latin America and elsewhere saw progress stagnate after experiencing considerable advances in the HAQ Index between 1990 and 2000. Striking subnational disparities emerged in personal health-care access and quality, with China and India having particularly large gaps between locations with the highest and lowest scores in 2016. In China, performance ranged from 91.5 (89.1-936) in Beijing to 48.0 (43.4-53.2) in Tibet (a 43.5-point difference), while India saw a 30.8-point disparity, from 64.8 (59.6-68.8) in Goa to 34.0 (30.3-38.1) in Assam. Japan recorded the smallest range in subnational HAQ performance in 2016 (a 4.8-point difference), whereas differences between subnational locations with the highest and lowest HAQ Index values were more than two times as high for the USA and three times as high for England. State-level gaps in the HAQ Index in Mexico somewhat narrowed from 1990 to 2016 (from a 20.9-point to 17.0-point difference), whereas in Brazil, disparities slightly increased across states during this time (a 17.2-point to 20.4-point difference). Performance on the HAQ Index showed strong linkages to overall development, with high and high-middle SDI countries generally having higher scores and faster gains for non-communicable diseases. Nonetheless, countries across the development spectrum saw substantial gains in some key health service areas from 2000 to 2016, most notably vaccine-preventable diseases. Overall, national performance on the HAQ Index was positively associated with higher levels of total health spending per capita, as well as health systems inputs, but these relationships were quite heterogeneous, particularly among low-to-middle SDI countries. Interpretation GBD 2016 provides a more detailed understanding of past success and current challenges in improving personal health-care access and quality worldwide. Despite substantial gains since 2000, many low-SDI and middle-SDI countries face considerable challenges unless heightened policy action and investments focus on advancing access to and quality of health care across key health services, especially non-communicable diseases. Stagnating or minimal improvements experienced by several low-middle to high-middle SDI countries could reflect the complexities of re-orienting both primary and secondary health-care services beyond the more limited foci of the Millennium Development Goals. Alongside initiatives to strengthen public health programmes, the pursuit of universal health coverage upon improving both access and quality worldwide, and thus requires adopting a more comprehensive view and subsequent provision of quality health care for all populations. Copyright (C) 2018 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.
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| 14. |
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| 15. |
- Huang, Xin, 1982-, et al.
(författare)
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Privacy of Value-Added Context-Aware Service Cloud
- 2009
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Ingår i: Lecture notes in computer science Volume 5931. - Berlin, Heidelberg : Springer. - 9783642106644 ; , s. 547-552
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Konferensbidrag (refereegranskat)abstract
- In the cloud computing era, service provider cloud and context service cloud store all your personal context data. This is a positive aspect for value-added context-aware service cloud as it makes that context information collection are easier than was the case previously. However, this computing environment does add a series of threats in relation to privacy protection. Whoever receives the context information is able to deduce the status of the owners and, generally owners are not happy to share this information. In this paper, we propose a privacy preserved framework which can be utilized by value-added context-aware service cloud. Context data and related services access privileges are determined by context-aware role-based access control (CRAC) extended from role-based access control (RAC). Privacy preserved context service protocol (PPCS) is designed to protect user privacy from exposed context information. Additionally, user network and information diffusion is combined to evaluate the privacy protection effect.
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| 16. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 17. |
- Kristan, Matej, et al.
(författare)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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Ingår i: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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| 18. |
- Lan, Lei, et al.
(författare)
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Medial ElasticsElastics: Efficient and Collision-Ready Deformation via Medial Axis Transform
- 2020
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Ingår i: ACM Transactions on Graphics. - : Association for Computing Machinery (ACM). - 1557-7368 .- 0730-0301. ; 39:3
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Tidskriftsartikel (refereegranskat)abstract
- We propose a framework for the interactive simulation of nonlinear deformable objects. The primary feature of our system is the seamless integration of deformable simulation and collision culling, which are often independently handled in existing animation systems. The bridge connecting them is the medial axis transform (MAT), a high-fidelity volumetric approximation of complex 3D shapes. From the physics simulation perspective, MAT leads to an expressive and compact reduced nonlinear model. We employ a semireduced projective dynamics formulation, which well captures high-frequency local deformations of high-resolution models while retaining a low computation cost. Our key observation is that the most compelling (nonlinear) deformable effects are enabled by the local constraints projection, which should not be aggressively reduced, and only apply model reduction at the global stage. From the collision detection (CD)/collision culling (CC) perspective, MAT is geometrically versatile using linear-interpolated spheres (i.e., the so-called medial primitives (MPs)) to approximate the boundary of the input model. The intersection test between two MPs is formulated as a quadratically constrained quadratic program problem. We give an algorithm to solve this problem exactly, which returns the deepest penetration between a pair of intersecting MPs. When coupled with spatial hashing, collision (including self-collision) can be efficiently identified on the GPU within a few milliseconds even for massive simulations. We have tested our system on a variety of geometrically complex and high-resolution deformable objects, and our system produces convincing animations with all of the collisions/self-collisions well handled at an interactive rate.
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| 19. |
- Lan, Ting, et al.
(författare)
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Extensive functional diversification of the Populus glutathione S-transferase supergene family
- 2009
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Ingår i: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 21:12, s. 3749-3766
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Tidskriftsartikel (refereegranskat)abstract
- Identifying how genes and their functions evolve after duplication is central to understanding gene family radiation. In this study, we systematically examined the functional diversification of the glutathione S-transferase (GST) gene family in Populus trichocarpa by integrating phylogeny, expression, substrate specificity, and enzyme kinetic data. GSTs are ubiquitous proteins in plants that play important roles in stress tolerance and detoxification metabolism. Genome annotation identified 81 GST genes in Populus that were divided into eight classes with distinct divergence in their evolutionary rate, gene structure, expression responses to abiotic stressors, and enzymatic properties of encoded proteins. In addition, when all the functional parameters were examined, clear divergence was observed within tandem clusters and between paralogous gene pairs, suggesting that subfunctionalization has taken place among duplicate genes. The two domains of GST proteins appear to have evolved under differential selective pressures. The C-terminal domain seems to have been subject to more relaxed functional constraints or divergent directional selection, which may have allowed rapid changes in substrate specificity, affinity, and activity, while maintaining the primary function of the enzyme. Our findings shed light on mechanisms that facilitate the retention of duplicate genes, which can result in a large gene family with a broad substrate spectrum and a wide range of reactivity toward different substrates.
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| 20. |
- Lan, Ting, et al.
(författare)
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Structural and Functional Evolution of Positively Selected Sites in Pine Glutathione S-Transferase Enzyme Family
- 2013
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 288:34, s. 24441-24451
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic analyses have identified positive selection as an important driver of protein evolution, both structural and functional. However, the lack of appropriate combined functional and structural assays has generally hindered attempts to elucidate patterns of positively selected sites and their effects on enzyme activity and substrate specificity. In this study we investigated the evolutionary divergence of the glutathione S-transferase (GST) family in Pinus tabuliformis, a pine that is widely distributed from northern to central China, including cold temperate and drought-stressed regions. GSTs play important roles in plant stress tolerance and detoxification. We cloned 44 GST genes from P. tabuliformis and found that 26 of the 44 belong to the largest (Tau) class of GSTs and are differentially expressed across tissues and developmental stages. Substitution models identified five positively selected sites in the Tau GSTs. To examine the functional significance of these positively selected sites, we applied protein structural modeling and site-directed mutagenesis. We found that four of the five positively selected sites significantly affect the enzyme activity and specificity; thus their variation broadens the GST family substrate spectrum. In addition, positive selection has mainly acted on secondary substrate binding sites or sites close to (but not directly at) the primary substrate binding site; thus their variation enables the acquisition of new catalytic functions without compromising the protein primary biochemical properties. Our study sheds light on selective aspects of the functional and structural divergence of the GST family in pine and other organisms.
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| 21. |
- Lan, Yihong, et al.
(författare)
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Dynamics of COVID-19 progression and the long-term influences of measures on pandemic outcomes
- 2022
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Ingår i: Emerging Themes in Epidemiology. - : BMC. - 1742-7622. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- The pandemic progression is a dynamic process, in which measures yield outcomes, and outcomes in turn influence subsequent measures and outcomes. Due to the dynamics of pandemic progression, it is challenging to analyse the long-term influence of an individual measure in the sequence on pandemic outcomes. To demonstrate the problem and find solutions, in this article, we study the first wave of the pandemic—probably the most dynamic period—in the Nordic countries and analyse the influences of the Swedish measures relative to the measures adopted by its neighbouring countries on COVID-19 mortality, general mortality, COVID-19 incidence, and unemployment. The design is a longitudinal observational study. The linear regressions based on the Poisson distribution or the binomial distribution are employed for the analysis. To show that analysis can be timely conducted, we use table data available during the first wave. We found that the early Swedish measure had a long-term and significant causal effect on public health outcomes and a certain degree of long-term mitigating causal effect on unemployment during the first wave, where the effect was measured by an increase of these outcomes under the Swedish measures relative to the measures adopted by the other Nordic countries. This information from the first wave has not been provided by available analyses but could have played an important role in combating the second wave. In conclusion, analysis based on table data may provide timely information about the dynamic progression of a pandemic and the long-term influence of an individual measure in the sequence on pandemic outcomes.
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| 22. |
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| 23. |
- Liang, Akun, et al.
(författare)
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High-Pressure Synthesis of Ultra-Incompressible, Hard and Superconducting Tungsten Nitrides
- 2024
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Ingår i: Advanced Functional Materials. - : WILEY-V C H VERLAG GMBH. - 1616-301X .- 1616-3028.
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Tidskriftsartikel (refereegranskat)abstract
- Transition metal nitrides, particularly those of 5d metals, are known for their outstanding properties, often relevant for industrial applications. Among these metal elements, tungsten is especially attractive given its low cost. In this high-pressure investigation of the W-N system, two novel ultra-incompressible tungsten nitride superconductors, namely W2N3 and W3N5, are successfully synthesized at 35 and 56 GPa, respectively, through a direct reaction between N2 and W in laser-heated diamond anvil cells. Their crystal structure is determined using synchrotron single-crystal X-ray diffraction. While the W2N3 solid's sole constituting nitrogen species are N3- units, W3N5 features both discrete N3- as well as N24- pernitride anions. The bulk modulus of W2N3 and W3N5 is experimentally determined to be 380(3) and 406(7) GPa, and their ultra-incompressible behavior is rationalized by their constituting WN7 polyhedra and their linkages. Importantly, both W2N3 and W3N5 are recoverable to ambient conditions and stable in air. Density functional theory calculations reveal W2N3 and W3N5 to have a Vickers hardness of 30 and 34 GPa, and superconducting transition temperatures at ambient pressure (50 GPa) of 11.6 K (9.8 K) and 9.4 K (7.2 K), respectively. Additionally, transport measurements performed at 50 GPa on W2N3 corroborate with the calculations. Two recoverable tungsten nitrides, namely W2N3 and W3N5, are synthesized using laser-heated diamond anvil cells. Both compounds exhibit a high bulk modulus, hardness, and superconducting transition temperature. image
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| 24. |
- Liao, XM, et al.
(författare)
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Vitamin D Enhances Neutrophil Generation and Function in Zebrafish (Danio rerio)
- 2022
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Ingår i: Journal of innate immunity. - : S. Karger AG. - 1662-8128 .- 1662-811X. ; 14:3, s. 229-242
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Tidskriftsartikel (refereegranskat)abstract
- Vitamin D (VD) is a major regulator of calcium metabolism in many living organisms. In addition, VD plays a key role in regulating innate and adaptive immunity in vertebrates. Neutrophils constitute an important part of the first line of defense against invading microbes; however, the potential effect of VD on neutrophils remains elusive. Thus, in this study zebrafish in different developmental stages were utilized to identify the potential role of VD in the basal homeostasis and functions of neutrophils. Our results showed that addition of exogenous VD<sub>3</sub> promoted granulopoiesis in zebrafish larvae. Reciprocally, neutrophil abundance in the intestine of adult zebrafish with a <i>cyp2r1</i> mutant, lacking the capacity to 25-hydroxylate VD, was reduced. Moreover, VD-mediated granulopoiesis was still observed in gnotobiotic zebrafish larvae, indicating that VD regulates neutrophil generation independent of the microbiota during early development. In contrast, VD was incapable to influence granulopoiesis in adult zebrafish when the commensal bacteria were depleted by antibiotic treatment, suggesting that VD might modulate neutrophil activity via different mechanisms depending on the developmental stage. In addition, we found that VD<sub>3</sub> augmented the expression of <i>il-8</i> and neutrophil recruitment to the site of caudal fin amputation. Finally, VD<sub>3</sub> treatment significantly decreased bacterial counts and mortality in zebrafish infected with <i>Edwardsiella tarda</i> (<i>E. tarda</i>) in a neutrophil-dependent manner. Combined, these findings demonstrate that VD regulates granulopoiesis and neutrophil function in zebrafish immunity.
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| 26. |
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| 27. |
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| 28. |
- Liu, Zhigang, et al.
(författare)
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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1, s. 855-
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Tidskriftsartikel (refereegranskat)abstract
- Cognitive decline is one of the complications of type 2 diabetes (T2D). Intermittent fasting (IF) is a promising dietary intervention for alleviating T2D symptoms, but its protective effect on diabetes-driven cognitive dysfunction remains elusive. Here, we find that a 28-day IF regimen for diabetic mice improves behavioral impairment via a microbiota-metabolites-brain axis: IF enhances mitochondrial biogenesis and energy metabolism gene expression in hippocampus, re-structures the gut microbiota, and improves microbial metabolites that are related to cognitive function. Moreover, strong connections are observed between IF affected genes, microbiota and metabolites, as assessed by integrative modelling. Removing gut microbiota with antibiotics partly abolishes the neuroprotective effects of IF. Administration of 3-indolepropionic acid, serotonin, short chain fatty acids or tauroursodeoxycholic acid shows a similar effect to IF in terms of improving cognitive function. Together, our study purports the microbiota-metabolites-brain axis as a mechanism that can enable therapeutic strategies against metabolism-implicated cognitive pathophysiologies.
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| 29. |
- Ramezani, Amir, et al.
(författare)
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A Pilot Evaluation of a Rapid Screening Test for Nosocomial Infection at a Neurosurgical Intensive Care Unit in Sweden
- 2020
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Ingår i: Point of Care. - : Lippincott Williams & Wilkins. - 1533-029X .- 1533-0303. ; 19:3, s. 63-71
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Tidskriftsartikel (refereegranskat)abstract
- Background: When postneurosurgery patients develop fever, there are no convenient methods to immediately indicate the site of infection. The choice of empirical antibiotic therapy is evidently different in nosocomial meningitis compared with ventilator-associated pneumonia or urinary tract infection. Conventional bacterial cultures run a risk of being false negative due to antibiotic prophylaxis, and direct microscopic analysis of cerebrospinal fluid (CSF) from such patients has limited diagnostic value. Because of the substantial mortality associated with nosocomial meningitis, broad spectrum antibiotics in high dosage are, therefore, commonly administered. Neutrophils as a part of the innate immunity system, trap and kill bacteria by neutrophil extracellular traps (NETs). Neutrophil extracellular traps are composed of extracellular DNA which is released to the CSF during bacterial meningitis. Using a combination of sulphated-glucosaminoglycan and aniline dyes, a measurement method was developed that reacts to extracellular host DNA and changes color within 1 minute in proportion to the amount of NETs in the body fluid tested. The present study aimed to evaluate the sensitivity and specificity of the "rapid NETs test" in identifying the site of infection. Methods: We performed analysis on the left-over CSF samples (n = 199) that were collected routinely at neurosurgical intensive care unit. No samples were included after patients were transferred to the ward. Besides CSF, bronchoalveolar fluid, and urine samples were collected in febrile patients. The "rapid NETs test" was used for simultaneous analysis of the fresh left-over samples. The final diagnosis was settled at discharge. Results: A total of 75 (64%) patients had received empirical antibiotic therapy against nosocomial meningitis, whereas only 19 patients of these cases (16%) had a verified diagnosis. The rapid NETs test could distinguish a verified meningitis (n = 19) with 89.5% sensitivity and 92.5% specificity. The test also identified ventilator-associated pneumonia (n = 32) with 93.8% sensitivity and 86.8% specificity. However, the test was not reliable in identifying nosocomial urinary tract infection (sensitivity and specificity, 78.6% and 55.2%, respectively). Conclusions: The rapid NETs test indicated the site of infection in febrile patients postneurosurgery with clinically relevant sensitivity and specificity, which might show its potential to minimize the unnecessary use of antibiotics.
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| 30. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 31. |
- Sandström, Camilla, Professor, 1967-, et al.
(författare)
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Administrando conflitos entre humanos e animais selvagens
- 2024. - 1
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Ingår i: Diretrizes da UICN CSE sobre conflitos e coexistência entre humanos e animais selvagens. - Gland : IUCN. - 9782831722559 ; , s. 83-88
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Bokkapitel (refereegranskat)
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| 32. |
- Sandström, Camilla, Professor, 1967-, et al.
(författare)
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Governing human-wildlife conflicts
- 2024. - 1
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Ingår i: IUCN SSC guidelines on human-wildlife conflict and coexistence. - Gland : IUCN. - 9782831722344 ; , s. 80-85
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Bokkapitel (refereegranskat)
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| 33. |
- Sandström, Camilla, Professor, 1967-, et al.
(författare)
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Réglementation des conflits entre les humains et la faune sauvage
- 2024. - 1
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Ingår i: Lignes directrices de l’UICN CSE sur les conflits entre les humains et la faune sauvage et sur leur coexistence. - Gland : IUCN. - 9782831722702 ; , s. 83-88
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Bokkapitel (refereegranskat)
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| 34. |
- Shi, Zhi Sheng, et al.
(författare)
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Enrichment of Ni–Mo–V via pyrometallurgical reduction from spent hydrogenation catalysts and the multi-reaction mechanism
- 2023
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Ingår i: Rare Metals. - 1001-0521 .- 1867-7185. ; 42:8, s. 2700-2712
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Tidskriftsartikel (refereegranskat)abstract
- Spent hydrogenation catalysts are important secondary resources due to richness in the valuable metals of Ni, Mo and V. Recovery of valuable metals from spent catalysts has high economic value and environmental benefits since they are hazardous wastes as well. Traditional recycling processes including hydrometallurgical leaching and soda roasting-leaching have disadvantages such as generating large amounts of wastewater, long process, and low recovery efficiency of valuable metals. Thus, this paper proposed synergistic enrichment of Ni, Mo and V via pyrometallurgical reduction at 1400–1500 °C. The melting temperature and viscosity of slag were reduced through slag designing by software FactSage 7.1. The phase diagram of Al2O3-CaO-SiO2-Na2O-B2O3 was drawn, and low-temperature region (≤ 1300 °C) was selected as target slag composition. Ni, Mo, and V can be collaborative captured and recovered through the mutual solubility at molten state. Increasing the melting temperature and the amount of CaO, Na2O and C were conducive to improving the metals recovery rates. The kilogram-scale experiments were carried out, and the recovery efficiencies of Ni, Mo and V were 98.3%, 95.3% and 97.9% under optimized conditions: at 1500 °C, with the basicity of 1.0, 13.1 wt% SiO2, 7.0 wt% B2O3, 7.7 wt% Na2O and 20.0 wt% C. The distribution behavior of valuable metals was clarified by investigating the melting process of slag and the reduction in valuable metals. Ni was preferentially reduced and acted as a capturing agent, which captured other metals to form NiMoV alloys. Graphical abstract: [Figure not available: see fulltext.]
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| 35. |
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| 36. |
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| 37. |
- Wang, Yaling, et al.
(författare)
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Enhanced performance and stability of inverted planar perovskite solar cells by incorporating 1,6-diaminohexane dihydrochloride additive
- 2018
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Ingår i: Solar Energy Materials and Solar Cells. - : ELSEVIER SCIENCE BV. - 0927-0248 .- 1879-3398. ; 188, s. 140-148
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Tidskriftsartikel (refereegranskat)abstract
- Herein, 1,6-Diaminohexane Dihydrochloride (1,6-DD) is introduced into perovskite precursors to fabricate the inverted planar perovskite solar cells. By regulating the concentration of 1,6-DD additive, the average power conversion efficiency (PCE) of perovskite solar cells is enhanced by 20%. The champion device achieves a relatively high PCE of 17% and an excellent fill factor of 80.1%. The PCE of the large-area (1 cm(2)) device also reaches to 13.68%. After exposure to the air for 16 days, the device with 1,6-DD additive still retains above 90% of the initial efficiency, exhibiting good stability. We demonstrate that a small amount of 1,6-DD affects the crystallization dynamic, yielding ideal perovskite film with enhanced crystallinity and enlarged grain size. The two terminal -NH3+ groups passivates the vacancy defects at the perovskite crystal surface, suppressing charge recombination and facilitating charge transportation effectively. Meanwhile, adjacent crystal surfaces are linked through the hexane alkyl chain of 1,6-DD molecule, which enhances the interaction between perovskite grains and anchors the microstructure of perovskite to some degree. Hydrophobic hexane alkyl chains also increase the moisture resistance of perovskite film. Thus, an easy and effective way is provided for fabricating efficient and stable perovskite solar cells.
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| 38. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 39. |
- Xie, Jiaying, et al.
(författare)
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STING activation in TET2-mutated hematopoietic stem/progenitor cells contributes to the increased self-renewal and neoplastic transformation
- 2023
-
Ingår i: Leukemia. - : Springer Nature. - 0887-6924 .- 1476-5551. ; 37:12, s. 2457-2467
-
Tidskriftsartikel (refereegranskat)abstract
- Somatic loss-of-function mutations of the dioxygenase Ten-eleven translocation-2 (TET2) occur frequently in individuals with clonal hematopoiesis (CH) and acute myeloid leukemia (AML). These common hematopoietic disorders can be recapitulated in mouse models. However, the underlying mechanisms by which the deficiency in TET2 promotes these disorders remain unclear. Here we show that the cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-stimulator of interferon genes (STING) pathway is activated to mediate the effect of TET2 deficiency in dysregulated hematopoiesis in mouse models. DNA damage arising in Tet2-deficient hematopoietic stem/progenitor cells (HSPCs) leads to activation of the cGAS-STING pathway which in turn promotes the enhanced self-renewal and development of CH. Notably, both pharmacological inhibition and genetic deletion of STING suppresses Tet2 mutation-induced aberrant hematopoiesis. In patient-derived xenograft (PDX) models, STING inhibition specifically attenuates the proliferation of leukemia cells from TET2-mutated individuals. These observations suggest that the development of CH associated with TET2 mutations is powered through chronic inflammation dependent on the activated cGAS-STING pathway and that STING may represent a potential target for intervention of relevant hematopoietic diseases.
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| 40. |
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| 41. |
- Yin, Lan, et al.
(författare)
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Chloroplast thylakoid transporters
- 2010
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Ingår i: The FEBS Journal. - : Wiley-Blackwell. - 1742-464X .- 1742-4658. ; 277:Suppl. 1, s. 231-231
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this study is to identify and functionally characterizesolute transporters from the chloroplast thylakoid membrane ofArabidopsis thaliana. As compared to chloroplast envelope transporters,much less information is available for transport processesacross the thylakoid membrane, which is mostly studied as thesite of light-driven photosynthetic reactions coupled to ATP synthesis.Although there are many reported examples of transportactivities, only a few thylakoid transporters have been identifiedat the gene level. Using bioinformatics analyses, we have predictedthe existence of approx. fifteen thylakoid transporters. Forexperimental validation, we have carried out immuno-localizationstudies used peptide-specific antibodies, functional analyses inheterologous system and validation using knockout mutants. Wehave recently identified one ATP/ADP carrier (Thuswaldneret al. JBC 2007) and one Na(+)-dependent phosphate transporter(Ruiz Pavon et al. JBC 2008). They are proposed to participatein the nucleotide metabolism in the thylakoid lumen(Spetea et al. PNAS 20004) as well as to balance the transthylakodproton electrochemical gradient storage. Based on phenotypicanalyses of knockout mutants, we will present novel dataabout the key physiological role of the two transporters duringthe high-light-induced repair of photosystem II complex in thethylakoid membrane. Subsequently, we will make a survey on theoutlook of thylakoid activities awaiting identification of responsibleproteins. Such knowledge is necessary to understand the thylakoidnetwork of transporters, and its role in photosynthesisand adaptation to environmental stress.
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| 42. |
- Yin, Lan, 1979
(författare)
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Molecular Mechanisms Optimizing Photosynthesis during High Light Stress in Plants
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Oxygenic photosynthesis is the process by which plants, algae and cyanobacteria use solar energy to convert water and carbon dioxide into molecular oxygen and carbohydrates. Photosynthesis sustains life on Earth since it provides not only energy for individual growth, but also represents the starting point of the food chain for most living organisms. Sunlight is essential for driving photosynthesis, but it is also known that in excess it can be stressful with severe consequences for plant growth. In this thesis I have used the model plant Arabidopsis thaliana to study molecular mechanisms optimizing photosynthesis during high light stress. One of these mechanisms is the reversible phosphorylation of proteins in the water-oxidizing photosystem II (PSII) complex. The serine/threonine-protein kinases STN7 and STN8 are involved in the phosphorylation of the PSII light-harvesting complex (LHCII) and core proteins, respectively. In Paper II, I found variation in the phosphorylation levels of these proteins in Arabidopsis natural accessions. In high light conditions, I found a correlation between the STN8 protein abundance and the D1 protein phosphorylation level. In growth light conditions, D1 and LHCII phosphorylation correlated with longitude, and in the case of LHCII phosphorylation with temperature variability as well. Another molecular mechanism for plants to overcome high light stress is via PSII repair. STN8- mediated PSII core phosphorylation is an early and crucial step for efficient PSII repair, since it alters the folding of the thylakoid membrane in a manner facilitating lateral migration of complexes to the sites of repair. Among three laboratory Arabidopsis accessions studied, Ws-4 displayed a reduced STN8 level resulting in decreased PSII core protein phosphorylation (Paper I). Nevertheless, the downstream steps in PSII repair proceeded normal or slightly faster. This phenomenon is probably due to compensatory mechanisms involving additional lipids and carotenoids to increase membrane fluidity and thus lateral migration of complexes. The thylakoid ATP/ADP carrier (TAAC) transports ATP into the thylakoid lumen for nucleotide-dependent reactions. In Paper III, I have found that TAAC- deficient plants displayed wild-type levels of PSII protein phosphorylation but slower disassembly of complexes and slower D1 protein degradation. I propose that ATP supplied by TAAC into the lumen is used for nucleotide-dependent reactions with roles in various steps of PSII repair. I have also found that, via its transport activity, TAAC may consume part of the proton gradient across the thylakoid membrane, which is critical for the initiation of photoprotective mechanisms. In a proteomics study of the stroma thylakoid membrane from Arabidopsis (Paper IV), I identified 58 proteins, including previously known ones as well as new putative thylakoid proteins with roles in photosynthesis transport, translation, protein fate, metabolism, stress response and signaling. This thesis deepens our understanding of photosynthetic regulation at the molecular level and improves the biochemical overview of the chloroplast thylakoid membrane.
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| 43. |
- Yin, Lan, 1979, et al.
(författare)
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Photosystem II Function and Dynamics in Three Widely Used Arabidopsis thaliana Accessions
- 2012
-
Ingår i: PLoS One. - : Public Library of Science (PLoS). - 1932-6203. ; 7:9
-
Tidskriftsartikel (refereegranskat)abstract
- Columbia-0 (Col-0), Wassilewskija-4 (Ws-4), and Landsberg erecta-0 (Ler-0) are used as background lines for many public Arabidopsis mutant collections, and for investigation in laboratory conditions of plant processes, including photosynthesis and response to high-intensity light (HL). The photosystem II (PSII) complex is sensitive to HL and requires repair to sustain its function. PSII repair is a multistep process controlled by numerous factors, including protein phosphorylation and thylakoid membrane stacking. Here we have characterized the function and dynamics of PSII complex under growth-light and HL conditions. Ws-4 displayed 30% more thylakoid lipids per chlorophyll and 40% less chlorophyll per carotenoid than Col-0 and Ler-0. There were no large differences in thylakoid stacking, photoprotection and relative levels of photosynthetic complexes among the three accessions. An increased efficiency of PSII closure was found in Ws-4 following illumination with saturation flashes or continuous light. Phosphorylation of the PSII D1/D2 proteins was reduced by 50% in Ws-4 as compared to Col-0 and Ler-0. An increase in abundance of the responsible STN8 kinase in response to HL treatment was found in all three accessions, but Ws-4 displayed 50% lower levels than Col-0 and Ler-0. Despite this, the HL treatment caused in Ws-4 the lagest extent of PSII inactivation, disassembly, D1 protein degradation, and the largest decrease in the size of stacked thylakoids. The dilution of chlorophyll-protein complexes with additional lipids and carotenoids in Ws-4 may represent a mechanism to facilitate lateral protein traffic in the membrane, thus compensating for the lack of a full complement of STN8 kinase. Nevertheless, additional PSII damage occurs in Ws-4, which exceeds the D1 protein synthesis capacity, thus leading to enhanced photoinhibition. Our findings are valuable for selection of appropriate background line for PSII characterization in Arabidopsis mutants, and also provide the first insights into natural variation of PSII protein phosphorylation.
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| 44. |
- Yin, Lan, et al.
(författare)
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Role of Thylakoid ATP/ADP Carrier in Photoinhibition and Photoprotection of Photosystem II in Arabidopsis
- 2010
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Ingår i: PLANT PHYSIOLOGY. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 153:2, s. 666-677
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Tidskriftsartikel (refereegranskat)abstract
- The chloroplast thylakoid ATP/ADP carrier (TAAC) belongs to the mitochondrial carrier superfamily and supplies the thylakoid lumen with stromal ATP in exchange for ADP. Here, we investigate the physiological consequences of TAAC depletion in Arabidopsis (Arabidopsis thaliana). We show that the deficiency of TAAC in two T-DNA insertion lines does not modify the chloroplast ultrastructure, the relative amounts of photosynthetic proteins, the pigment composition, and the photosynthetic activity. Under growth light conditions, the mutants initially displayed similar shoot weight, but lower when reaching full development, and were less tolerant to high light conditions in comparison with the wild type. These observations prompted us to study in more detail the effects of TAAC depletion on photoinhibition and photoprotection of the photosystem II (PSII) complex. The steady-state phosphorylation levels of PSII proteins were not affected, but the degradation of the reaction center II D1 protein was blocked, and decreased amounts of CP43-less PSII monomers were detected in the mutants. Besides this, the mutant leaves displayed a transiently higher nonphotochemical quenching of chlorophyll fluorescence than the wild-type leaves, especially at low light. This may be attributed to the accumulation in the absence of TAAC of a higher electrochemical H+ gradient in the first minutes of illumination, which more efficiently activates photoprotective xanthophyll cycle-dependent and independent mechanisms. Based on these results, we propose that TAAC plays a critical role in the disassembly steps during PSII repair and in addition may balance the trans-thylakoid electrochemical H+ gradient storage.
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| 45. |
- Yin, Lan, 1979, et al.
(författare)
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The membrane proteome of stroma thylakoids from Arabidopsis thaliana studied by successive in-solution and in-gel digestion.
- 2015
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Ingår i: Physiologia Plantarum : An International Journal for Plant Biology. - : Wiley. - 0031-9317 .- 1399-3054. ; 154:3, s. 433-446
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Tidskriftsartikel (refereegranskat)abstract
- From individual localization and large-scale proteomic studies, we know that stroma-exposed thylakoid membranes harbor part of the machinery performing the light-dependent photosynthetic reactions. The minor components of the stroma thylakoid proteome, regulating and maintaining the photosynthetic machinery, are in the process of being unraveled. In this study, we developed in-solution and in-gel proteolytic digestion methods, and used them to identify minor membrane proteins, e.g. transporters, in stroma thylakoids prepared from Arabidopsis thaliana (L.) Heynh Columbia-0 leaves. In-solution digestion with chymotrypsin yielded the largest number of peptides, but in combination with methanol extraction resulted in identification of the largest number of membrane proteins. Although less efficient in extracting peptides, in-gel digestion with trypsin and chymotrypsin led to identification of additional proteins. We identified a total of 58 proteins including 44 membrane proteins. Almost half are known thylakoid proteins with roles in photosynthetic light reactions, proteolysis and import. The other half, including many transporters, are not known as chloroplast proteins, because they have been either curated (manually assigned) to other cellular compartments or not curated at all at the plastid protein databases. Transporters include ATP-binding cassette (ABC) proteins, transporters for K+ and other cations. Other proteins either have a role in processes probably linked to photosynthesis, namely translation, metabolism, stress and signaling or are contaminants. Our results indicate that all these proteins are present in stroma thylakoids; however, individual studies are required to validate their location and putative roles. This study also provides strategies complementary to traditional methods for identification of membrane proteins from other cellular compartments.
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| 46. |
- Yin, Zekun, et al.
(författare)
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Computing Platforms for Big Biological Data Analytics : Perspectives and Challenges
- 2017
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Ingår i: Computational and Structural Biotechnology Journal. - : Elsevier. - 2001-0370. ; 15, s. 403-411
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Tidskriftsartikel (refereegranskat)abstract
- The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.
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| 47. |
- Örtegren Kugelberg, Unn, 1975-, et al.
(författare)
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Separation and characterization of caveolae subclasses in the plasma membrane of primary adipocytes : segregation of specific proteins and functions
- 2006
-
Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 273:14, s. 3381-3392
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Tidskriftsartikel (refereegranskat)abstract
- Caveolae are nearly ubiquitous plasma membrane domains that in adipocytes vary in size between 25 and 150 nm. They constitute sites of entry into the cell as well as platforms for cell signalling. We have previously reported that plasma membrane-associated caveolae that lack cell surface access can be identified by electron microscopy. We now report the identification, after density gradient ultracentrifugation, of a subclass of very high-density apparently closed caveolae that were not labelled by cell surface protein labelling of intact cells. These caveolae contained caveolin-1 and caveolin-2. Another class of high-density caveolae contained caveolin-1, caveolin-2 and specifically fatty acid transport protein-1, fatty acid transport protein-4, fatty acyl-CoA synthetase, hormone-sensitive lipase, perilipin, and insulin-regulated glucose transporter-4. This class of caveolae was specialized in fatty acid uptake and conversion to triacylglycerol. A third class of low-density caveolae contained the insulin receptor, class B scavenger receptor-1, and insulin-regulated glucose transporter-4. Small amounts of these proteins were also detected in the high-density caveolae. In response to insulin, the insulin receptor autophosphorylation and the amount of insulin-regulated glucose transporter-4 increased in these caveolae. The molar ratio of cholesterol to phospholipid in the three caveolae classes varied considerably, from 0.4 in very high-density caveolae to 0.9 in low-density caveolae. There was no correlation between the caveolar contents of caveolin and cholesterol. The low-density caveolae, with the highest cholesterol concentration, were particularly enriched with the cholesterol-rich lipoprotein receptor class B scavenger receptor-1, which mediated cholesteryl ester uptake from high-density lipoprotein and generation of free cholesterol in these caveolae, suggesting a specific role in cholesterol uptake/metabolism. These findings demonstrate a segregation of functions in caveolae subclasses.
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